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Correct link formatting in vignettes
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pratikunterwegs committed Apr 23, 2024
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2 changes: 1 addition & 1 deletion vignettes/epidemics.Rmd
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Expand Up @@ -43,7 +43,7 @@ Prepare population and contact data.
::: {.alert .alert-info}
### Note on social contacts data {-}

**Note that** the social contacts matrices provided by the _socialmixr_[https://CRAN.R-project.org/package=socialmixr] package follow a format wherein the matrix $M_{ij}$ represents [contacts from group $i$ to group $j$](https://epiforecasts.io/socialmixr/articles/socialmixr.html#usage).
**Note that** the social contacts matrices provided by the [_socialmixr_](https://CRAN.R-project.org/package=socialmixr) package follow a format wherein the matrix $M_{ij}$ represents [contacts from group $i$ to group $j$](https://epiforecasts.io/socialmixr/articles/socialmixr.html#usage).

However, epidemic models traditionally adopt the notation that $M_{ij}$ defines contacts to $i$ from $j$ [@wallinga2006].

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2 changes: 1 addition & 1 deletion vignettes/modelling_interventions.Rmd
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Expand Up @@ -37,7 +37,7 @@ Prepare population and contact data.

_epidemics_ expects social contacts matrices $M_{ij}$ to represent contacts to $i$ from $j$ [@wallinga2006], such that $q M_{ij} / n_i$ is the probability of infection, where $q$ is a scaling factor dependent on infection transmissibility, and $n_i$ is the population proportion of group $i$.

Social contacts matrices provided by the _socialmixr_[https://CRAN.R-project.org/package=socialmixr] package follow the opposite convention, where $M_{ij}$ represents [contacts from group $i$ to group $j$](https://epiforecasts.io/socialmixr/articles/socialmixr.html#usage).
Social contacts matrices provided by the [_socialmixr_](https://CRAN.R-project.org/package=socialmixr) package follow the opposite convention, where $M_{ij}$ represents [contacts from group $i$ to group $j$](https://epiforecasts.io/socialmixr/articles/socialmixr.html#usage).

Thus social contact matrices from _socialmixr_ need to be transposed (using `t()`) before they are used with _epidemics_.
:::
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